Patrick A. D. Grimont

Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology

An ad hoc committee for the re-evaluation of the species definition in bacteriology met in Gent, Belgium, in February 2002. The committee made various recommendations regarding the species definition in the light of developments in methodologies available to systematists.

Delineation of Borrelia burgdorferi Sensu Stricto, Borrelia garinii sp. nov., and Group VS461 Associated with Lyme Borreliosis

We studied 48 Borrelia isolates that were associated with Lyme borreliosis or were isolated from ticks and identified three DNA relatedness groups by using the S1 nuclease method. The three DNA groups (genospecies) were associated with specific rRNA gene restriction patterns, protein electrophoresis patterns, and patterns of reactivity with murine monoclonal antibodies. Genospecies I corresponded to Borrelia burgdorferi sensu stricto since it contained the type strain of this species (strain ATCC 35210); this genospecies included 28 isolates from Europe and the United States. Genospecies II was named Borrelia garinii sp. nov. and included 13 isolates from Europe and Japan. Genospecies III (group VS461) included seven isolates from Europe and Japan.

Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates

ABSTRACT A multilocus sequence typing (MLST) scheme was developed for Klebsiella pneumoniae. Sequences of seven housekeeping genes were obtained for 67 K. pneumoniae strains, including 19 ceftazidime- and ciprofloxacin-resistant isolates. Forty distinct allelic profiles were identified. MLST data were validated against ribotyping and showed high (96%) discriminatory power. The MLST approach provides unambiguous data useful for the epidemiology of K. pneumoniae isolates.

Brucella, a Monospecific Genus as Shown by Deoxyribonucleic Acid Hybridization

A total of 51 strains (including type, reference, vaccine, and field strains) representing all species and biovars of Brucella formed a single deoxyribonucleic acid-deoxyribonucleic acid hybridization group (S1 nuclease method). Accordingly, we propose that only one species, Brucella melitensis, be recognized in the genus. We recommend that other specific epithets formerly associated with the generic name Brucella be used in a vernacular form for biovar designation (e.g., Brucella melitensis biovar Abortus 1).

Staphylococcus lugdunensis sp. nov. and Staphylococcus schleiferi sp. nov., Two Species from Human Clinical Specimens

Deoxyribonucleic acid relatedness studies (S1 nuclease method) showed that 23 unidentified Staphylococcus strains form two homogeneous genomic species related 1 to 9% to 24 type strains representing known Staphylococcus species. These new species were named Staphylococcus lugdunensis and Staphylococcus schleiferi. Strains of S. lugdunensis were susceptible to novobiocin, produced a fibrinogen affinity factor, and failed to produce coagulase, heat-stable nuclease, and staphylokinase. S. lugdunensis strains differed from S. hominis (the phenotypically closest species) by production of ornithine decarboxylase and the fibrinogen affinity factor. The guanine-plus-cytosine content of the deoxyribonucleic acid was 32 mol%. The type strain is N860297 (= ATCC 43809). Strains of S. schleiferi were susceptible to novobiocin, produced a heat-stable nuclease and a fibrinogen affinity factor, and failed to produce coagulase and staphylokinase. S. schleiferi strains differed from S. aureus by production of an antigenically different heat-stable nuclease and the lack of pigmentation, free coagulase, protein A, and β-ribitol teichoic acid. The guanine-plus-cytosine content of the deoxyribonucleic acid was 37 mol%. The type strain is N850274 (= ATCC 43808).

Emergence of Extended-Spectrum-β-Lactamase (CTX-M-9)-Producing Multiresistant Strains of Salmonella enterica Serotype Virchow in Poultry and Humans in France

ABSTRACT During 2002 to 2003, eight Salmonella enterica serotype Virchow poultry and poultry product isolates from various sources (chicken farms, poultry slaughterhouse, or retail store) and one S. enterica rough strain isolated from human feces were found to produce extended-spectrum β-lactamase CTX-M-9. Poultry and poultry product isolates were recovered from different locations in the southwest of France. The human rough isolate had sequences of flagellin genes (fliC and fljB) typical of serotype Virchow and ribotyping and pulsed-field gel electrophoresis (PFGE) patterns closely similar to those of serotype Virchow strains. PFGE confirmed the clonal relationship between the poultry isolates, while the human isolate displayed a pattern with 94% homology. The blaCTX-M-9 gene was located on a conjugative plasmid and was shown to be linked to orf513. Plasmid profiling found a very similar EcoRI restriction pattern in six transconjugants studied, including transconjugants obtained from the human isolate. A single hatchery, supplying chicks to the six farms, was identified. Emergence of extended-spectrum β-lactamase-producing S. enterica strains in food animals is a major concern, as such strains could disseminate on a large scale and lead to antibiotic therapy difficulties.

Clonal Emergence of Extended-Spectrum β-Lactamase (CTX-M-2)-Producing Salmonella enterica Serovar Virchow Isolates with Reduced Susceptibilities to Ciprofloxacin among Poultry and Humans in Belgium and France (2000 to 2003)

ABSTRACT Antibiotic treatment is not required in cases of Salmonella enterica gastroenteritis but is essential in cases of enteric fever or invasive salmonellosis or in immunocompromised patients. Although fluoroquinolones and extended-spectrum cephalosporins are the drugs of choice to treat invasive Salmonella, resistance to these antibiotics is increasing worldwide. During the period 2000 to 2003, 90 Salmonella enterica serovar Virchow poultry and poultry product isolates and 11 serovar Virchow human isolates were found to produce an extended-spectrum β-lactamase, CTX-M-2, concomitantly with a TEM-1 β-lactamase. The blaCTX-M-2 gene was located on a large conjugative plasmid (>100 kb). Pulsed-field gel electrophoresis indicated a clonal relationship between the poultry and human isolates. All these isolates displayed additional resistance to trimethoprim-sulfamethoxazole and tetracycline as well as a reduced susceptibility to ciprofloxacin (MICs of between 0.5 and 1 μg/ml). CTX-M-2-producing Salmonella with a reduced susceptibility to fluoroquinolones constitutes a major concern, since such strains could disseminate on a large scale and jeopardize classical antibiotic therapy in immunocompromised patients.

Deoxyribonucleic Acid Relatedness and Phenotypic Characterization of Flexibacter columnaris sp. nov., nom. rev., Flexibacter psychrophilus sp. nov., nom. rev., and Flexibacter maritimus Wakabayashi, Hikida, and Masumura 1986

Eight unidentified fish pathogens and 10 strains received as “Flexibacter columnaris,” “Cytophaga psychrophila,” and Flexibacter maritimus were compared with the type strains of all previously described species in the genera Cytophaga and Flexibacter and with seven Flavobacterium species by determining levels of deoxyribonucleic acid (DNA) relatedness (S1 nuclease method) and by performing phenotypic tests. The name Flexibacter columnaris sp. nov. is revived for a DNA relatedness group comprising eight strains that are 75 to 100% related to strain TG 39/87 and 0 to 8% related to all of the other species studied. These strains produce flat rhizoid colonies which adhere to agar, show strong gliding movement, absorb Congo red, reduce nitrate to nitrite, and produce H2S. The guanine-plus-cytosine content of the DNA is 32 mol%. The type strain is strain NCMB 2248 (= ATCC 23463). The name Flexibacter psychrophilus sp. nov. is revived for a DNA relatedness group comprising seven strains that are 90 to 100% related to strain NCMB 1947T (T = type strain) and 0 to 5% related to all of the other species studied. These strains produce circular, convex colonies that have regular or spreading margins and do not adhere to agar, show very slow gliding movement, do not absorb Congo red, do not reduce nitrate, and do not produce H2S. The guanine-plus-cytosine content of the DNA is 33 mol%. The type strain is strain NCMB 1947. Both F. columnaris and F. psychrophilus produce the flexirubin type of pigments, are strongly proteolytic, and do not hydrolyze (or produce acid from) any carbohydrate. Flexibacter maritimus (three strains) was shown to constitute a DNA relatedness group that is 0 to 8% related to all of the other species tested. Furthermore, this organism can be differentiated by phenotypic tests. The presence of F. maritimus in Europe is shown for the first time.

Classification of citrobacteria by DNA hybridization: designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and three unnamed Citrobacter genomospecies.

DNA relatedness studies (hydroxyapatite method) were done on 112 strains of citrobacteria. By using the recommended definition of a genomospecies 11 genomospecies were identified in the genus Citrobacter. These genomospecies were separable by their biochemical profiles. Citrobacter koseri (Citrobacter diversus) and Citrobacter amalonaticus proved to be homogeneous species, as previously described. C. amalonaticus biogroup 1, as described by Farmer et al. (J. Clin. Microbiol. 21:46-76, 1985), was shown to be a separate homogeneous species, which was named Citrobacter farmeri sp. nov. The Citrobacter freundii complex was quite heterogeneous. C. freundii sensu stricto, as represented by the type strain, contained only 9 of 66 strains in this complex. The remaining 57 strains were members of seven genomospecies. Genomospecies 5, containing 21 strains, was named Citrobacter youngae sp. nov. Genomospecies 6, containing 15 strains, was named Citrobacter braakii sp. nov. Genomospecies 7 and 8, each containing six strains, were named Citrobacter werkmanii sp. nov. and Citrobacter sedlakii sp. nov., respectively. Genomospecies 9, 10, and 11, each containing three strains, were not named.

SHV-12-like extended-spectrum-β-lactamase-producing strains of Salmonella enterica serotypes Babelsberg and Enteritidis isolated in France among infants adopted from Mali

ABSTRACT From December 2002 to June 2003, 14 cultures of Salmonella enterica serotype Babelsberg and 6 cultures of serotype Enteritidis, isolated in France from internationally adopted children, were identified at the French National Reference Center for Salmonella. All serotype Babelsberg isolates were related, as determined by pulsed-field gel electrophoresis, and all serotype Enteritidis strains displayed the same phage type. All serotype Enteritidis and seven serotype Babelsberg isolates produced an SHV-12-like extended-spectrum β-lactamase as determined by sequencing of PCR products and by isoelectrofocusing. Some serotype Enteritidis isolates exhibited additional antimicrobial resistance (aminoglycosides, tetracycline, chloramphenicol, sulfonamides, and trimethoprim). Our investigation indicated that these Salmonella isolates were certainly acquired in the same orphanage in Bamako, Mali, before the children were adopted by French families. An inappropriate use of ceftriaxone was probably the cause of the emergence of such strains. There is an urgent need to determine the origin of the contamination and to introduce adequate antibiotic protocols into this orphanage to prevent further transmission and dissemination. Screening for infections and follow-up, adapted to the origin of the internationally adopted children, should be recommended.